Blast Protein tool: threading

[Tom Goddard]

The following bug report has been submitted:
Platform:        Linux-5.3.0-45-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.93 (2020-04-03)
Description
I am unable to use the Blast Protein tool. Where one is supposed to insert the sequence allignments or protein sequence, the software does not allow you to paste anything. I was also hoping that I could run the jobs using multithreading.

Log:
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show "Blast Protein"

> help help:quickstart

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

Expected an objects specifier or a view name or a keyword  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> ui autostart false "Model Panel"

Expected a models specifier or a keyword  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

QObject::startTimer: Timers can only be used with threads started with QThread  

QObject::startTimer: Timers can only be used with threads started with QThread  

> toolshed show "Modeller Comparative"

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> toolshed show "Blast Protein"

> help help:user

> toolshed show "Modeller Comparative"




OpenGL version: 3.3 (Core Profile) Mesa 19.2.8
OpenGL renderer: llvmpipe (LLVM 9.0, 256 bits)
OpenGL vendor: VMware, Inc.
Manufacturer: Dell Inc.
Model: PowerEdge R520
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2450L 0 @ 1.80GHz
Cache Size: 20480 KB
Graphics:
	06:00.0 VGA compatible controller [0300]: Matrox Electronics Systems Ltd. G200eR2 [102b:0534]
	Subsystem: Dell G200eR2 [1028:04f6]
	Kernel driver in use: mgag200

[Eric Pettersen]

Reported by Karl Voigtritter

[Conrad Huang]

Currently, the Blast Protein tool can only use the sequence from a chain in an opened model as the query.

An alternative is to open your sequence (FASTA format works) and then used the "blast {sequence_name}" command. For FASTA format, "{sequence_name}" is the label on the description line that starts with >.

[Elaine Meng]

This is an RFE not a bug report. Request is to allow entering sequence directly into the Blast Protein GUI, like can be done in Chimera.

[Conrad Huang]

Blasting against a sequence in Chimera can only be done by entering the sequence, but ChimeraX supports opening sequence files. Once opened, the sequences can be used in blast searches, although only from the command line. So the question is whether we should add a blast GUI to sequence viewer, or continue to support entering a sequence via blastprotein.

[Elaine Meng]

There is another option, like what we had in Chimera: Blast Protein GUI allows pasting a sequence in as the query.

[Zach Pearson]

I think it would be good to consider the threading issue separately from arbitrary sequence input, which is now part of #5055

[Zach Pearson]

I've never used ChimeraX < 1.2.5, so I'm not sure what BlastProtein was like for 0.93 (the version from the user's report).

If the blastprotein tool's new UI could be run multiple times without hanging the UI while waiting for results, would this ticket be obsolete?

[Tom Goddard]

I don't think this ticket is about multithreading -- why the reporter mentioned that is unclear. There question was about pasting in a sequence which the current and past GUIs did not allow. It may be worth allowing pasting in a sequence -- the AlphaFold GUI is an example that allows that.

[Zach Pearson]

As of tonight's daily build, several instances of the blastprotein command can now be run at the same time (whether from the command line or from the GUI), and results windows will independently display themselves afterwards. I think this _probably_ satisfies the multithreading ask. I realize I forgot to add the user to #5055 -- will add.

[Elaine Meng]

This ticket is NOT about multithreading. It is about pasting plain text sequence into the Blast dialog. Structural biologists refer to finding 3D structures consistent with a sequence as "threading."

[Eric Pettersen]

Reporter email address no longer valid, so changed to goddard (same as #5055). I could be wrong, but this ticket looks to be originally about both pasted sequence input and multithreading and this ticket became the "multithreading" one and #5055 became the "pasted sequence input" one.

[Zach Pearson]

What's the expectation here, is it running several separate BLAST jobs from one interface given several sequences, or is it running all the sequences in the same BLAST job?

[Tom Goddard]

The reporter was Karl Voigtritter from 2.5 years ago. It seems like his description is clear enough, he didn't know where to enter a sequence because he could not paste in anything to the user interface. And the multithreading part very likely means running blast froze ChimeraX at that time (ChimeraX 0.93). The blocking of ChimeraX was long ago fixed. Perhaps your recent changes allow pasting in a sequence.

[Zach Pearson]

They do. :)